*Please try out the new RNA-Seq analysis workflow included in RobiNA and help us make it more useful by sending us your feedback concerning bugs, missing features etc. Thanks!

THE LATEST VERSION OF ROBINA AT LEAST ON WINDOWS SEEMS TO ERROUNSLY CONCATENATES GZ FILES IN THE ALIGNMENT STEP

We are currently looking into this, until then, please unzip files manually.

Several commercial programs such as GeneSpring featuring a rich and simple user interface to statistically analyze high-throughput "omics" data are available. However, these are usually very expensive and might even require an annual subscription. On the other hand, there are free, open source tools such as BioConductor which offer great statistical options and support for free, but this power often comes at the price of usability, since these tools often feature either only a command line interface or solely very basic user interaction. Finally, there are tools such as RMA Express which offer a rich user interface but only a very limited set of options.

RobiNA tries to bridge this gap by providing a flexible user friendly graphical interface to unleash the power of R/BioConductor for the individual biologist. RobiNA comes as a convenient all-in-one installation package, that automatically installs the application itself plus all required external tools (i.e. the R and BioConductor frameworks and bowtie).

Currently, using RobiNA it is possible to analyse Illumina/Solexa-based RNA-Seq data (supplied in FASTQ format), Affymetrix data and generic tabular two color or single channel array data.

Furthermore, RobiNA offers a variety of quality control methods that can be used to gain an overview of the experimental data technical quality and structure. Using the built-in graphical experiment designer, researchers can define which samples to compare (even combinations of samples are possible) and finally produce a comprehensive set of tables and plots giving detailed results of the experiment such as the log fold change (M), average expression (A) values at a (user-adjustable) probability for differential expression. Tables summarizing information on the top 100 differentially regulated genes and several plots visualizing the quality of each chip or RNA-Seq library are also generated. The results can directly be imported into MapMan and PageMan for visualization and further analysis.

RobiNA was developed for min. Java version 6. If the Java runtime environment is not installed on your system, the installer packages will detect this and direct you to a download source for Java automatically.

A RNA-Seq dataset that can be used for testing RobiNA can be downloadedhere. The archive contains: 1)A sample of raw sequence data obtained from the study SRP009936 as deposited in the European Nucleotide Archive (ENA) 2)The current arabidopsis transcriptome (TAIR10 cds) to be used as the reference in the mapping step.

3) The current arabidopsis genome release (TAIR10_all_chr.fas) plus the corresponding GFF3 annotation file to be used as reference genome in the mapping step.

Mac OSX 10.8 (Mountain Lion)

When starting RobiNA on Mac OS X 10.8.x by double-clicking, the operating system displays a dialog that implies that the software is damaged and should be deleted. That, however, is not the case. The reason for this behaviour is the new security mechanism, called GateKeeper, that was introduced in Mac OS 10.8 and that blocks any application that was not signed by an Apple-certified developer and distributed via the App Store from execution. Users experiencing this problem, please read this thread for details on how to bypass this problem. We are currently considering how to deal with this in the future.

Important notice to Windows users

Please download the installer package that matches the Java Virtual Machine (JVM) installed on your system irrespective of the underlying operating system. If you have a 32-bit JVM installed on a 64-bit Windows 7 you'll need the 32-bit installer package.

Required Java version moved to 6 SE

Due to internal changes and updates, the Robin application now requires Java version 6 SE (standard edition). Please be sure to update the Java version installed on your system - sorry for the inconvenience.